\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0903223470:

Variant ID: vg0903223470 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 3223470
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGACATGCCACCACGACATACCGGAAAGAGGCCGTGACAGGACCCTTCGCATAACCCCCTCTAGCCAAGCACACCACACCTCAGGTTTCACCCCCGTCCC[T/C]
AGCGAGCAACGGGCAGTCCCCTCTCGTGCCTAGGTGAATCCGGAAGCGACAGAGGCCGTCGCAGGGCCCGCCCCGCTCCATCACGCCCACCTTTGCCTGG

Reverse complement sequence

CCAGGCAAAGGTGGGCGTGATGGAGCGGGGCGGGCCCTGCGACGGCCTCTGTCGCTTCCGGATTCACCTAGGCACGAGAGGGGACTGCCCGTTGCTCGCT[A/G]
GGGACGGGGGTGAAACCTGAGGTGTGGTGTGCTTGGCTAGAGGGGGTTATGCGAAGGGTCCTGTCACGGCCTCTTTCCGGTATGTCGTGGTGGCATGTCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.70% 29.00% 14.39% 3.94% NA
All Indica  2759 56.30% 13.50% 23.56% 6.63% NA
All Japonica  1512 35.60% 64.20% 0.20% 0.00% NA
Aus  269 92.90% 1.50% 4.46% 1.12% NA
Indica I  595 51.90% 11.80% 30.25% 6.05% NA
Indica II  465 44.30% 15.70% 26.45% 13.55% NA
Indica III  913 67.50% 12.70% 17.31% 2.52% NA
Indica Intermediate  786 53.80% 14.40% 24.05% 7.76% NA
Temperate Japonica  767 2.50% 97.30% 0.26% 0.00% NA
Tropical Japonica  504 79.60% 20.20% 0.20% 0.00% NA
Japonica Intermediate  241 49.40% 50.60% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 57.80% 25.60% 16.67% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0903223470 T -> DEL N N silent_mutation Average:38.463; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 N N N N
vg0903223470 T -> C LOC_Os09g06760.1 upstream_gene_variant ; 2253.0bp to feature; MODIFIER silent_mutation Average:38.463; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 N N N N
vg0903223470 T -> C LOC_Os09g06750-LOC_Os09g06760 intergenic_region ; MODIFIER silent_mutation Average:38.463; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0903223470 NA 1.08E-10 mr1084 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0903223470 NA 3.28E-13 mr1205 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0903223470 NA 8.08E-12 mr1206 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0903223470 NA 1.76E-07 mr1206 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0903223470 NA 4.38E-07 mr1220 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0903223470 NA 4.98E-07 mr1229 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0903223470 2.24E-06 6.45E-11 mr1596 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0903223470 NA 8.45E-07 mr1596 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0903223470 NA 5.43E-07 mr1880 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0903223470 NA 6.79E-07 mr1042_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0903223470 NA 7.75E-06 mr1206_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0903223470 NA 2.76E-06 mr1359_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0903223470 NA 5.62E-14 mr1593_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251